A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus - PubMed (original) (raw)

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus

Erin P Westeen et al. J Hered. 2023.

Abstract

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

Keywords: CCGP; California Conservation Genomics Project; Dipsadinae; conservation genetics; reference genome; snake.

© The American Genetic Association. 2023.

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Figures

Fig. 1.

Fig. 1.

(A) Range map of Diadophis punctatus in California showing the morphological subspecies boundaries as defined by Blanchard (1942), though recent work by Fontanella et al. (2021) found evidence for only three lineages in the state. (B) An individual from California showing the characteristic ring-neck coloration, bright red ventral coloration, and tail curling behavior (D. p. amabilis or Western California Lineage). (C) Another individual lacking characteristic the ring-neck coloration, displaying some of the variation in ventral coloration present in D. punctatus, and exhibiting tail curling behavior (D. p. regalis).

Fig. 2.

Fig. 2.

Visual overview of genome assembly metrics. (A) K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome. K-mers covered at lower coverage and lower frequency correspond to differences between haplotypes, whereas the higher coverage and higher frequency k-mers correspond to the similarities between haplotypes. (B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the Diadophis punctatus primary assembly (rDiaPun1). The plot circle represents the full size of the assembly. From the inside out, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly. The dark vs. light blue area around it shows mean, maximum, and minimum GC vs. AT content at 0.1% intervals (Challis et al. 2020). (C and D) Omni-C Contact maps for the primary (2C) and alternate (2D) genome assembly generated with PretextSnapshot. Omni-C contact maps translate proximity of genomic regions in 3-D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two of such regions. Scaffolds are separated by black lines and higher density corresponds to higher levels of fragmentation.

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